Variant report

Variant	rs4291502
Chromosome Location	chr1:151413180-151413181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151412036..151414559-chr1:151416954..151420193,3	MCF-7	breast:
2	1:151411623-151426875..1:151592347-151603110	GM12878	blood:
3	1:151171193-151178589..1:151411623-151426875	GM12878	blood:
4	chr1:151411812..151418574-chr1:151428106..151433466,11	MCF-7	breast:
5	chr1:151410628..151413374-chr1:151426124..151427883,2	MCF-7	breast:
6	chr1:151411841..151424302-chr1:151427210..151433048,24	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143398	Chromatin interaction
ENSG00000206635	Chromatin interaction
ENSG00000143442	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10736380	0.84[CEU][hapmap]
rs11204819	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[MKK][hapmap]
rs11204824	0.84[CEU][hapmap]
rs11801791	0.83[CEU][hapmap]
rs12025432	0.84[CEU][hapmap]
rs12730283	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12743850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12747749	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751531	0.84[CEU][hapmap]
rs12760638	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1780583	0.86[AMR][1000 genomes]
rs1887544	0.84[CEU][hapmap]
rs1887545	0.84[CEU][hapmap]
rs2025899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2495380	0.81[CEU][hapmap]
rs3748550	0.84[CEU][hapmap]
rs4246527	0.84[CEU][hapmap]
rs4603	0.84[CEU][hapmap]
rs4971043	0.84[CEU][hapmap]
rs4971047	0.84[CEU][hapmap]
rs6587572	0.84[CEU][hapmap]
rs6587577	0.84[CEU][hapmap]
rs6587584	0.84[CEU][hapmap]
rs6684333	0.84[CEU][hapmap]
rs71515781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71515782	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546151	0.84[CEU][hapmap]
rs9436029	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv872424	chr1:151325055-151413180	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv872425	chr1:151325055-151413790	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv872429	chr1:151329138-151413180	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv463827	chr1:151333167-151413180	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv547850	chr1:151333167-151413180	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv872430	chr1:151334796-151413180	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv872431	chr1:151338570-151413180	Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv872432	chr1:151339196-151413180	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv872433	chr1:151341417-151413180	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv872434	chr1:151347820-151413180	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv872435	chr1:151351060-151413180	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	32 gene(s)	inside rSNPs	diseases
14	nsv872436	chr1:151357333-151413180	Genic enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	32 gene(s)	inside rSNPs	diseases
15	nsv872437	chr1:151373065-151413180	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
16	nsv872438	chr1:151377407-151413180	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
17	nsv872440	chr1:151396037-151413180	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
18	esv1811070	chr1:151403570-151433317	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4291502	SPRR2B	cis	parietal	SCAN
rs4291502	SELENBP1	cis	Thyroid	GTEx
rs4291502	POGZ	cis	cerebellum	SCAN
rs4291502	TCHH	cis	cerebellum	SCAN
rs4291502	S100A13	cis	cerebellum	SCAN
rs4291502	SELENBP1	cis	cerebellum	SCAN
rs4291502	MRPS21	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151373400-151416400	Weak transcription	Stomach Mucosa	stomach
2	chr1:151393000-151413400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:151398400-151429600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:151398600-151417400	Weak transcription	Fetal Heart	heart
5	chr1:151400800-151417400	Weak transcription	Aorta	Aorta
6	chr1:151401000-151416200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:151401000-151430000	Weak transcription	Esophagus	oesophagus
8	chr1:151401400-151413200	Weak transcription	Small Intestine	intestine
9	chr1:151401400-151417400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:151401600-151429200	Weak transcription	Spleen	Spleen
11	chr1:151402200-151413200	Weak transcription	Fetal Brain Male	brain
12	chr1:151402200-151416200	Weak transcription	Colonic Mucosa	Colon
13	chr1:151403200-151413200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:151403200-151413200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:151403200-151413200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:151403200-151413400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:151403200-151413400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:151403200-151413400	Weak transcription	Fetal Kidney	kidney
19	chr1:151403200-151413800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:151403200-151416800	Weak transcription	HSMMtube	muscle
21	chr1:151403400-151413200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:151403400-151413200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:151403400-151413200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:151403400-151413200	Weak transcription	HUVEC	blood vessel
25	chr1:151403400-151413400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:151403400-151413400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:151403400-151413400	Weak transcription	Pancreas	Pancrea
28	chr1:151403400-151416200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:151403600-151413200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:151403800-151413200	Weak transcription	NH-A	brain
31	chr1:151405800-151428400	Weak transcription	Right Atrium	heart
32	chr1:151406000-151415800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:151406200-151414800	Strong transcription	Dnd41	blood
34	chr1:151406400-151415200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:151408200-151413200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:151408200-151413400	Weak transcription	NHLF	lung
37	chr1:151408400-151413200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:151408400-151413200	Weak transcription	NHDF-Ad	bronchial
39	chr1:151408400-151413200	Weak transcription	Osteobl	bone
40	chr1:151408400-151416200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:151408800-151414600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:151408800-151414600	Strong transcription	Fetal Intestine Large	intestine
43	chr1:151408800-151414800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:151408800-151414800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:151409000-151415000	Strong transcription	Placenta	Placenta
46	chr1:151409200-151414000	Strong transcription	Thymus	Thymus
47	chr1:151409200-151414200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:151409200-151414400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:151409200-151415000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:151409200-151415200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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